Re: ImageJ/Fiji Memory issues - actually an OSX disk image misunderstanding problem

Posted by Barron, Francie on Jul 20, 2010; 4:40pm
URL: http://imagej.273.s1.nabble.com/Re-ImageJ-Fiji-Memory-issues-actually-an-OSX-disk-image-misunderstanding-problem-tp3687536p3687537.html

Hi Daniel,

Thanks for the information.  Yes, I had forgot that I was running from the .dmg/disk image file since I fell prey to the updater bug on OSX and did not realize there was a fix.  I deleted and redownloaded an updated Fiji version and all was fixed!  

Thanks again for the information!
~Francie

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Francie Barron (Hyndman), Graduate Student
Cells Biology, Stem Cells, and Development Program
Dr. David Clouthier lab, Craniofacial Biology

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________________________________________
From: Daniel James White [[hidden email]]
Sent: Tuesday, July 20, 2010 3:37 AM
To: ImageJ Interest Group
Cc: Barron, Francie
Subject: Re: ImageJ/Fiji Memory issues - actually an OSX  disk image misunderstanding problem

Hi Francie,

On Jul 19, 2010, at 6:01 AM, IMAGEJ automatic digest system wrote:

> Date:    Sun, 18 Jul 2010 20:48:35 -0600
> From:    "Barron, Francie" <[hidden email]>
> Subject: Re: ImageJ/Fuji Memory issues
>
> Hey All,
>
> I've tried to increase the memory available in my FIJI program (via edit --> options --> Memory and Threads) to 1600mb (which is what my ImageJ program has it set for).  I get this error:
>
> Could not write /Volumes/Fiji/Fiji.app/Contents/Info.plist

Very common problem... its a misunderstanding of how diskimages work on OSX:

the problem you see is because you are running Fiji from the mounted disk image that you down loaded.
You should not do that. If you want to change the settings, it tries to write the changes to the disk image, - but that is NOT writable.

What you should do is (common procedure for OSX software):

download the Fiji from the website
OSX will get the disk image and mount it as a disk - and it will appear on your desktop. (if not, you can double click the downloaded .dmg file)
There is an instruction in that finder window for you to drag and drop fiji into your applications folder.
You should do that!

Dont run Fiji from the mounted disk image, but drag and drop (copy)  it into your applications folder,

When its done copying, unmount the disk image ("Eject it - by clicking on the little arrow next to it in a finder window, or by dragging it to the trash)

Now you can also add Fiji to your dock by dragging it there from your applications folder (not from the mounted disk image)

remember to update your fiji often:  Help - update fiji

>
> Anyone know how to fix this issue?

hope the above fixed the problem in your understanding of disk images....
I have seem many people make the same error - its not really obvious enough, one place where OSX does not  "just work"

> I'm trying to run TrekEM2 in order to do montages.  It has been working fine, but recently has been crashing due to Java running out of memory.

there is no sunstitute for more memory here....
if you machine only has 2GB, you can pretty much forget about dealing with more image dasta than that limit.

you need a workstation with an order of magnitude more RAM to do many jobs at a reasonable speed.


cheers

Dan



>
> Any help would be great.
>
> Thanks!
> ~Francie
>
> NOTE NEW EMAIL ADDRESS:  [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

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